S4 cleanup

.Rbuildignore

@@ -8,3 +8,4 @@
 ^\.pixi
 ^.covrignore
 ^.claude
+^data-raw$

.covrignore

@@ -1,2 +1,4 @@
 .pixi
 /tmp/pixi/.pixi
+R/deprecated.R
+R/exampleData.R

.github/recipe/recipe.yaml

@@ -45,6 +45,7 @@ requirements:
     - r-colocboost
     - r-cpp11
     - r-cpp11armadillo
+    - r-ctwas
     - r-decor
     - r-dplyr
     - r-flashier
@@ -73,6 +74,7 @@ requirements:
     - r-readr
     - r-rfast
     - r-rlang
+    - r-robustbase
     - r-softimpute
     - r-stringr
     - r-susier
@@ -104,6 +106,7 @@ requirements:
     - r-colocboost
     - r-cpp11
     - r-cpp11armadillo
+    - r-ctwas
     - r-decor
     - r-dplyr
     - r-flashier
@@ -132,6 +135,7 @@ requirements:
     - r-readr
     - r-rfast
     - r-rlang
+    - r-robustbase
     - r-softimpute
     - r-stringr
     - r-susier

DESCRIPTION

@@ -71,6 +71,7 @@ Suggests:
     Rfast,
     RcppDPR,
     rmarkdown,
+    robustbase,
     rtracklayer,
     SNPRelate,
     snpStats,
@@ -88,46 +89,55 @@ VignetteBuilder: knitr
 Config/roxygen2/version: 8.0.0
 RoxygenNote: 7.3.3
 Collate:
-    'AllClasses.R'
-    'AllGenerics.R'
-    'AllMethods.R'
-    'LD.R'
-    'allele_qc.R'
-    'colocboost_pipeline.R'
-    'compute_qtl_enrichment.R'
+    'allGenerics.R'
+    'AnnotationMatrix.R'
+    'FineMappingEntry.R'
+    'FineMappingResultBase.R'
+    'GenotypeHandle.R'
+    'tupleSelectors.R'
+    'GwasFineMappingResult.R'
+    'H2Estimate.R'
+    'LdBlocks.R'
+    'LdData.R'
+    'LdStatistic.R'
+    'LdEigen.R'
+    'LdScore.R'
+    'QtlDataset.R'
+    'MultiStudyQtlDataset.R'
+    'QtlFineMappingResult.R'
+    'SumStatsBase.R'
+    'TwasWeightsEntry.R'
+    'causalInferencePipeline.R'
+    'colocPipeline.R'
+    'colocboostPipeline.R'
     'cpp11.R'
-    'ctwas_wrapper.R'
-    'dentist_qc.R'
-    'encoloc.R'
-    'example_data.R'
-    'file_utils.R'
-    'fsusie_wrapper.R'
-    'genotype_io.R'
-    'gwas_sumstats.R'
-    'h2_annotations.R'
-    'h2_estimate_wrappers.R'
-    'h2_gldsc.R'
-    'h2_hdl.R'
-    'h2_lder.R'
-    'h2_utils.R'
-    'ld_loader.R'
-    'mash_wrapper.R'
-    'misc.R'
-    'mr.R'
-    'mrmash_wrapper.R'
-    'multitrait_data.R'
-    'multivariate_pipeline.R'
-    'pval_combine.R'
-    'raiss.R'
-    'regularized_regression.R'
-    'relatedness_qc.R'
-    'slalom.R'
-    'sldsc_wrapper.R'
-    'sumstats_qc.R'
-    'susie_wrapper.R'
-    'twas.R'
-    'twas_weights.R'
-    'univariate_pipeline.R'
-    'univariate_rss_diagnostics.R'
-    'variant_id.R'
-    'vcf_writer.R'
+    'ctwasPipeline.R'
+    'ctwasWrapper.R'
+    'deprecated.R'
+    'exampleData.R'
+    'fineMappingPipeline.R'
+    'fineMappingWrappers.R'
+    'genotypeIo.R'
+    'gwasSumStats.R'
+    'h2Annotations.R'
+    'h2EstimationWrappers.R'
+    'jointDispatchers.R'
+    'jointSpecification.R'
+    'ld.R'
+    'mashPipeline.R'
+    'mashWrapper.R'
+    'pvalCombine.R'
+    'qtlEnrichmentPipeline.R'
+    'qtlSumStats.R'
+    'regularizedRegressionWrappers.R'
+    'relatednessQc.R'
+    'sldscPostprocessingPipeline.R'
+    'sldscWrapper.R'
+    'sumstatsQc.R'
+    'twasWeights.R'
+    'twasWeightsPipeline.R'
+    'variantId.R'
+    'vcfWriter.R'
+Depends: 
+    R (>= 3.5)
+LazyData: true